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(-) Description

Title :  STRUCTURE OF THE ARMADILLO REPEAT DOMAIN OF PLAKOPHILIN 1
 
Authors :  H. J. Choi, W. I. Weis
Date :  01 Oct 04  (Deposition) - 22 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Armadillo Repeat, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. J. Choi, W. I. Weis
Structure Of The Armadillo Repeat Domain Of Plakophilin 1.
J. Mol. Biol. V. 346 367 2005
PubMed-ID: 15663951  |  Reference-DOI: 10.1016/J.JMB.2004.11.048
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PLAKOPHILIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentARMADILLO REPEAT DOMAIN
    GenePKP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1XM9)

(-) Sites  (0, 0)

(no "Site" information available for 1XM9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XM9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XM9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_062171A463VPKP1_HUMANPolymorphism10920171AA442V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARM_REPEATPS50176 Armadillo/plakoglobin ARM repeat profile.PKP1_HUMAN287-314
329-372
595-623
  3A:287-314
A:329-372
A:574-602

(-) Exons   (10, 10)

Asymmetric/Biological Unit (10, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003528451bENSE00001434679chr1:201252831-201253032202PKP1_HUMAN1-68680--
1.2ENST000003528452ENSE00000791344chr1:201263070-201263173104PKP1_HUMAN68-102350--
1.3ENST000003528453ENSE00000791345chr1:201282294-201282688395PKP1_HUMAN103-2341320--
1.5ENST000003528455ENSE00001192836chr1:201285681-201285825145PKP1_HUMAN234-282491A:244-28239
1.6ENST000003528456ENSE00000791348chr1:201286700-201286907208PKP1_HUMAN283-352701A:283-35270
1.7ENST000003528457ENSE00000791349chr1:201287746-201287923178PKP1_HUMAN352-411601A:352-411 (gaps)60
1.8aENST000003528458aENSE00001074129chr1:201288944-20128900663PKP1_HUMAN411-432221A:411-4111
1.9ENST000003528459ENSE00000791350chr1:201289395-201289509115PKP1_HUMAN432-470391A:412-44938
1.10ENST0000035284510ENSE00000791351chr1:201291106-201291261156PKP1_HUMAN471-522521A:450-48031
1.11ENST0000035284511ENSE00000791353chr1:201292141-201292317177PKP1_HUMAN523-581591A:509-56052
1.12ENST0000035284512ENSE00000523184chr1:201293556-201293709154PKP1_HUMAN582-633521A:561-61252
1.13ENST0000035284513ENSE00000523189chr1:201294069-201294255187PKP1_HUMAN633-695631A:612-67463
1.14ENST0000035284514ENSE00000791356chr1:201294882-20129496685PKP1_HUMAN695-723291A:674-70027
1.15bENST0000035284515bENSE00001435420chr1:201297890-20129796475PKP1_HUMAN724-747240--

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:420
 aligned with PKP1_HUMAN | Q13835 from UniProtKB/Swiss-Prot  Length:747

    Alignment length:478
                                   253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713        
           PKP1_HUMAN   244 GLTIPKAVQYLSSQDEKYQAIGAYYIQHTCFQDESAKQQVYQLGGICKLVDLLRSPNQNVQQAAAGALRNLVFRSTTNKLETRRQNGIREAVSLLRRTGNAEIQKQLTGLLWNLSSTDELKEELIADALPVLADRVIIPFSGWCDGNSNMSREVVDPEVFFNATGCLRKRLGMRELLALVPQRATSSRVNLSSADAGRQTMRNYSGLIDSLMAYVQNCVAASRCDDKSVENCMCVLHNLSYRLDAEVPTRYRQLEYNARNAYTEKSSTGCFSNKSDKMMNNNYDCPLPEEETNPKGSGWLYHSDAIRTYLNLMGKSKKDATLEACAGALQNLTASKGLMSSGMSQLIGLKEKGLPQIARLLQSGNSDVVRSGASLLSNMSRHPLLHRVMGNQVFPEVTRLLTSHTGNTSNSEDILSSACYTVRNLMASQPQLAKQYFSSSMLNNIINLCRSSASPKAAEAARLLLSDMWSSKELQGVL 721
               SCOP domains d1xm9a1 A:244-700 Plakophilin 1                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------Arm-1xm9A01 A:276-316                    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..---------..hhhhhhhhhhhhh---------------------hhh.hhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhh.hhhhhhhhh.----------------------------........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------ARM_REPEAT  PDB: A:287-314  --------------ARM_REPEAT  PDB: A:329-372 UniProt: 329-372 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ARM_REPEAT  PDB: A:574-602   -------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: A:244-282 [INCOMPLETE]  Exon 1.6  PDB: A:283-352 UniProt: 283-352                             ----------------------------------------------------------Exon 1.8a [INCOMPLETE]--------------------------------------Exon 1.10  PDB: A:450-480 UniProt: 471-522          Exon 1.11  PDB: A:509-560 UniProt: 523-581 [INCOMPLETE]    Exon 1.12  PDB: A:561-612 UniProt: 582-633          -------------------------------------------------------------Exon 1.14  PDB: A:674-700   Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: A:352-411 (gaps) UniProt: 352-411            --------------------Exon 1.9  PDB: A:412-449 [INCOMPLETE]  ------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.13  PDB: A:612-674 UniProt: 633-695                     -------------------------- Transcript 1 (2)
                 1xm9 A 244 GLTIPKAVQYLSSQDEKYQAIGAYYIQHTCFQDESAKQQVYQLGGICKLVDLLRSPNQNVQQAAAGALRNLVFRSTTNKLETRRQNGIREAVSLLRRTGNAEIQKQLTGLLWNLSSTDELKEELIADALPVLADRVIIPFSGWC---------VVDPEVFFNATGCLR---------------------NLSSADAGRQTMRNYSGLIDSLMAYVQNCVAASRCDDKSVENCMCVLHNLSYRLDAEVPTRYRQLEYNA----------------------------LPEEETNPKGSGWLYHSDAIRTYLNLMGKSKKDATLEACAGALQNLTASKGLMSSGMSQLIGLKEKGLPQIARLLQSGNSDVVRSGASLLSNMSRHPLLHRVMGNQVFPEVTRLLTSHTGNTSNSEDILSSACYTVRNLMASQPQLAKQYFSSSMLNNIINLCRSSASPKAAEAARLLLSDMWSSKELQGVL 700
                                   253       263       273       283       293       303       313       323       333       343       353       363       373       383   |     -   |   403       | -         -       412       422       432       442       452       462       472       | -         -         -      |512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692        
                                                                                                                                                                         387       397           411                   412                                                                 480                          509                                                                                                                                                                                               

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1XM9)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: TPR (230)
(-)
Family: Arm (24)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PKP1_HUMAN | Q13835)
molecular function
    GO:0019215    intermediate filament binding    Interacting selectively and non-covalently with an intermediate filament, a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of higher eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space.
    GO:0005521    lamin binding    Interacting selectively and non-covalently with lamin; any of a group of intermediate-filament proteins that form the fibrous matrix on the inner surface of the nuclear envelope.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    GO:0030280    structural constituent of epidermis    The action of a molecule that contributes to the structural integrity of an epidermal cutaneous structure.
biological process
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0045110    intermediate filament bundle assembly    The formation of the bundles of intermediate filaments. Intermediate filament-associated proteins (IFAPs) cross-link intermediate filaments with one another, forming a bundle or a network, and with other cell structures, including the plasma membrane. The organization of intermediate filaments and their supportive function in various cells types depends in large part on their linkage to other cell structures via IFAPs.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0016337    single organismal cell-cell adhesion    The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism.
cellular component
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0030057    desmosome    A cell-cell junction in which: on the cytoplasmic surface of each interacting plasma membrane is a dense plaque composed of a mixture of intracellular anchor proteins; a bundle of keratin intermediate filaments is attached to the surface of each plaque; transmembrane adhesion proteins of the cadherin family bind to the plaques and interact through their extracellular domains to hold the adjacent membranes together by a Ca2+-dependent mechanism.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005882    intermediate filament    A cytoskeletal structure that forms a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: Type I, acidic keratins; Type II, basic keratins; Type III, including desmin, vimentin and others; Type IV, neurofilaments and related filaments; and Type V, lamins.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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